The gastrointestinal epithelium is one of the most proliferative/regenerative tissues in adult organisms pointing to the existence of an intestinal stem cell (ISC) pool. Progress towards identification, isolation, and study of a self-renewing, multipotential intestinal stem cell has been hindered thus far due to the following factors: a) the lack of specific intestinal stem cell markers, b) the lack of a full understanding of the molecular mechanisms that the intestinal stem cell uses to choose between self-maintenance or differentiation, and c) a lack of methods to isolate intestinal stem cells and characterize them at the molecular and physiologic level. Identifying the intestinal stem cell and defining the molecular mechanisms that underlie intestinal stem/progenitor cell potency is critical to the understanding of both normal and dysregulated intestinal function. Recently, the SOX-family of transcription factors has been implicated in modulating stem or progenitor cell potency and competence - the ability to self-renew and differentiate into all cell types of the tissue/organ. The mRNAs for several SOX family members have been detected in both the adult small intestine and colon. With the exception of SOX9 the cellular localization and role of SOX factors in the intestine remain largely unknown. SOX9 has been localized to what is widely thought to be the stem cell niche in the small intestine. The broad expression pattern of SOX9 at the base of the crypt suggests it is a biomarker of both stem and progenitor cells. We have recently demonstrated that SOX4 and SOX7 expression is more restricted in small intestine to a very small population of cells in the small intestine stem cell niche. Thus, the central hypothesis of this study is that specific SOX proteins are biomarkers of stem and progenitor crypt cells in the intestine and play a critical role in maintaining stem/progenitor cell potency and competence. To test this hypothesis I propose the following aims: 1) To establish an expression profile for SOX family members in stem and progenitor cells, 2) To use chromatin immunoprecipitation (ChIP) and a novel Sox9EGFP reporter mouse to define the functional role of SOX9. 3) To develop a dual purpose red- fluorescent protein/lineage marking mouse model (Sox4Tomato/CreERT2) to assay 'sternness'of Sox4 [sic] - expressing cells. These studies are critical to enhance our understanding and treatment of intestinal injury and repair, congenital disorders, and cancer.